In your $HOME/.cpan/prefs you can hold .yml files that describe how cpan should act on the distributions describes in the YAML file, which includes answering questions asked by Makefile.PL or Build.PL. You can make sections specific for os, so these preferences can be shipped portable across OS's. These files can also refer to patches that you want to apply to the modules (for various reasons). These patches are usually stored in $HOME/.cpan/patches.